Hi Evan, One approach is to save your marker set, then open another copy of it. It is not currently possible to duplicate the marker set without saving it. The newly opened copy is a new marker set, with its own model number, and Chimera commands like "select 1", "move z 5.7", "turn z 30.0" could then be used to shift and rotate the copy, and the Path tracer dialog menu entry Actions / Transfer markers could be used to merge the markers into a single marker set. That is pretty tedious. A better approach is to use a Python script. I've attached one that copies markers from the active marker set to make any number of repeats. You use it by placing markers and then just open the script with File / Open to build the helix. The helix parameters (rotation, rise, repeats) are set in the script. For schematically showing a structure "fall apart" it may be fine to hand move the atoms. If you wanted it to fall apart in a defined way you could modify the above script to move markers instead of copy them. Is it ok if I post your previous message to chimera-users? Tom J. Evan Sadler wrote:

Tom,

I'm trying to use Chimera to make schematic 3D figures for publication.

One example is constructing a model of a structure, starting with a 3D reconstruction from negative stain EM. I can place spheres or cylinders in the map and make a representation of the repeating unit in, say, a helical tubule composed of self-assembling proteins. Knowing the axial rise and the pitch, I could build a model by translating/rotating repeating units, if that were possible.

Also, this particular helical tubule is held together by low pH and calcium ions. When if falls apart, one could illustrate this by translating individual markers.

I can do all this, rather tediously, by temporarily putting markers in different sets, which can be made active or inactive for movement from the command line. I was hoping to save a lot of keystrokes by using move or turn on individually specified objects. The mouse of course can move atoms, but is not precise enough for what I want to do.

Evan

On 8/2/07 1:08 PM, "Thomas Goddard" <goddard@cgl.ucsf.edu> wrote:

...

Hi Evan,

There is no Chimera command to move individual markers (or atoms). Could you tell me in what situation you would use this capability?

Tom

# ---------------------------------------------------------------------------- # Copy the markers in the active marker set to build a helix. # def make_z_helix(rotation, translation, repeats): import VolumePath as vp d = vp.volume_path_dialog() mset = d.active_marker_set mlist = mset.markers() # mlist = mset.selected_markers() # Copy only the selected markers. from math import sin, cos, pi from PDBmatrices.matrices import apply_matrix for r in range(repeats): a = (r+1) * rotation * pi / 180 mt = ((cos(a), -sin(a), 0, 0), (sin(a), cos(a), 0, 0), (0, 0, 1, (r+1)*translation)) for m in mlist: xyz = apply_matrix(mt, m.xyz()) mset.place_marker(xyz, m.rgba(), m.radius()) # ---------------------------------------------------------------------------- # make_z_helix(rotation = 30, # degrees translation = 2.5, repeats = 10)